Variant report
| Variant | rs12080669 |
|---|---|
| Chromosome Location | chr1:220526759-220526760 |
| allele | C/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:0)
- CpG islands (count:0)
- Chromatin interactive region (count:1)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
| No data |
| No data |
(count:1 , 50 per page) page:
1
| No. | Distal block | Cell Line | Cell type | Cell Stage |
|---|---|---|---|---|
| 1 | chr1:220524929..220526776-chr1:220534314..220536728,2 | MCF-7 | breast: |
| No data |
| No data |
| No data |
| No data |
rSNPs within LD-proxies of this variant (count:12)
| rs_ID | r2[population] |
|---|---|
| rs55874043 | 0.81[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs60326603 | 0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes] |
| rs73092160 | 0.96[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs73095644 | 0.81[AMR][1000 genomes];0.81[EUR][1000 genomes] |
| rs73101290 | 1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs73102536 | 0.81[AMR][1000 genomes];0.87[EUR][1000 genomes] |
| rs73103010 | 1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs73103020 | 0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs73103022 | 0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes] |
| rs73103033 | 1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs73104956 | 1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs7550884 | 0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | nsv1001681 | chr1:220425057-220548325 | Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
| 2 | nsv535298 | chr1:220425057-220548325 | Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' | TF binding regionCpG islandChromatin interactive regionlncRNA | 9 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:38)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs12080669 | PPARG | trans | lymphoblastoid | seeQTL |
| rs12080669 | PTPRK | trans | lymphoblastoid | seeQTL |
| rs12080669 | CRYM | trans | lymphoblastoid | seeQTL |
| rs12080669 | BASP1 | trans | lymphoblastoid | seeQTL |
| rs12080669 | IL28RA | trans | lymphoblastoid | seeQTL |
| rs12080669 | RHOU | trans | lymphoblastoid | seeQTL |
| rs12080669 | C1orf106 | trans | lymphoblastoid | seeQTL |
| rs12080669 | GRM8 | trans | lymphoblastoid | seeQTL |
| rs12080669 | MTTP | trans | lymphoblastoid | seeQTL |
| rs12080669 | SGMS2 | trans | lymphoblastoid | seeQTL |
| rs12080669 | MYRIP | trans | lymphoblastoid | seeQTL |
| rs12080669 | GCNT1 | trans | lymphoblastoid | seeQTL |
| rs12080669 | ANO10 | trans | lymphoblastoid | seeQTL |
| rs12080669 | HNF1B | trans | lymphoblastoid | seeQTL |
| rs12080669 | LRRC1 | trans | lymphoblastoid | seeQTL |
| rs12080669 | ACSM3 | trans | lymphoblastoid | seeQTL |
| rs12080669 | PLD1 | trans | lymphoblastoid | seeQTL |
| rs12080669 | CD79B | trans | lymphoblastoid | seeQTL |
| rs12080669 | TNFRSF11A | trans | lymphoblastoid | seeQTL |
| rs12080669 | SLC44A2 | trans | lymphoblastoid | seeQTL |
| rs12080669 | ANXA4 | trans | lymphoblastoid | seeQTL |
| rs12080669 | STEAP2 | trans | lymphoblastoid | seeQTL |
| rs12080669 | TBC1D4 | trans | lymphoblastoid | seeQTL |
| rs12080669 | RNF217 | trans | lymphoblastoid | seeQTL |
| rs12080669 | BCAS3 | trans | lymphoblastoid | seeQTL |
| rs12080669 | GAS2 | trans | lymphoblastoid | seeQTL |
| rs12080669 | PARD3 | trans | lymphoblastoid | seeQTL |
| rs12080669 | RASA1 | trans | lymphoblastoid | seeQTL |
| rs12080669 | SMARCA2 | trans | lymphoblastoid | seeQTL |
| rs12080669 | ARPC5L | trans | lymphoblastoid | seeQTL |
| rs12080669 | LRRK2 | trans | lymphoblastoid | seeQTL |
| rs12080669 | CHST2 | trans | lymphoblastoid | seeQTL |
| rs12080669 | IFNA2 | trans | lymphoblastoid | seeQTL |
| rs12080669 | CSRP2 | trans | lymphoblastoid | seeQTL |
| rs12080669 | TGFBR3 | trans | lymphoblastoid | seeQTL |
| rs12080669 | C14orf105 | trans | lymphoblastoid | seeQTL |
| rs12080669 | EPS8 | trans | lymphoblastoid | seeQTL |
| rs12080669 | TNFRSF21 | trans | lymphoblastoid | seeQTL |
| No. | Chromosome Location | Chromatin state | Cell line | Tissue |
|---|---|---|---|---|
| 1 | chr1:220524000-220526800 | Weak transcription | HUES6 Cell Line | embryonic stem cell |
| 2 | chr1:220524400-220526800 | Weak transcription | ES-I3 Cell Line | embryonic stem cell |
| 3 | chr1:220526400-220527000 | Enhancers | iPS DF 19.11 Cell Line | embryonic stem cell |
| 4 | chr1:220526600-220527000 | Enhancers | H9 Cell Line | embryonic stem cell |
| 5 | chr1:220526600-220527000 | Enhancers | iPS DF 6.9 Cell Line | embryonic stem cell |
| 6 | chr1:220526600-220527200 | Enhancers | ES-UCSF4 Cell Line | embryonic stem cell |
